[ADAM-322] Adding ADAMFeatureField for projections over ADAMFeature.

For some reason, we'd neglected to include an ADAMFeatureField class in the adam.projections
package!  This commit fixes that.
[ADAM-307] Fixing Features2ADAM so that it can be run from the CLI.

Features2ADAM fails because it doesn't include an 'index' field in its
second command-line argument, and therefore Args4j can't parse the Features2ADAMArgs
object off a command line.

This commit adds the missing 'index' argument to the Features2ADAMArgs class.

There is a test for this additional feature -- however, that test is marked as IGNORE
because we can't get it to work either locally or on Jenkins.  This should be addressed,
and I'll open up a ticket for it.  In the meantime, however, we've verified that manually
that this patch works as advertised.

Also modified PrintADAM to use the scala.Console.out rather than System.out.
This seems to allow us to (in tests) redirect the output stream using the
Console.withOut command.
Merge pull request #308 from genomebridge/features2adam-bug

Fixing the 'index 0' bug in features2adam
[maven-release-plugin] prepare release adam-parent-0.12.1
[maven-release-plugin] prepare for next development iteration
[ADAM-324] Adding documentation for commit/issue nomenclature and rebasing.
Merge pull request #325 from fnothaft/issue-docs

Adding documentation for commit/issue nomenclature and rebasing
[ADAM-326] Adding a 5-second retry on the HttpRangedByteAccess test.

The AMPLab webserver that is used in the test occasionally hangs?  If so, we catch
the HttpHostConnectException that the Apache lib throws, wait five seconds, and try
once more.
Merge pull request #328 from genomebridge/adam-326

[ADAM-326] Adding a 5-second retry on the HttpRangedByteAccess test.
[ADAM-294] Replacing shade plugin with appassembler.
[ADAM-316] Adding native Java language bindings for ADAM.
Reformatting pom's to match Maven's 2 space indent convention (see http://maven.apache.org/developers/conventions/code.html)
[ADAM-318] Added code coverage capture via scoverage.
add count of mismatches to mdtag
Merge pull request #329 from hammerlab/mdtag-counts

Add count of mismatches to mdtag
Added the TrackedLayout class.
Added filterByOverlappingRegion to AdamRDDFunctions
Added the VizReads tool to CLI.

VizReads is a tool for interactive or static visualization of aligned reads along the genome.
Ran ./scripts/format-source